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  1. UGENE
  2. UGENE-4036

MSA performance: remove columns of gaps

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.16
    • Component/s: Basic-MSA
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-19/02/2015
    • Affect Type:
      Userdefined

      Description

      1. Open "_common_data/clustal/gap_column.aln".
      2. MSA sequence area context menu -> Edit -> Remove columns of gaps.
      3. Choose "Remove all gap-only columns".
      4. Click "Remove".
      UGENE 1.16-dev: it take ~15 minutes to remove gaps.
      UGENE 1.15.1: it takes ~5 seconds to remove gaps.

      Fix the performance problem.

      This problem is a blocker because removing of gap columns is used in Sanger alignment feature - one of the main features of UGENE 1.16.

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            People

            Assignee:
            iprotsyuk Ivan Protsyuk
            Reporter:
            ggrekhov German Grekhov
            Assigned Tester:
            Artyom Savchenko
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved:

                Time Tracking

                Estimated:
                Original Estimate - 5 hours
                5h
                Remaining:
                Remaining Estimate - 5 hours
                5h
                Logged:
                Time Spent - Not Specified
                Not Specified